Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia

Rani, Lata; Mathur, Nitin; Gupta, Ritu; Gogia, Ajay; Kaur, Gurvinder; Dhanjal, Jaspreet Kaur; Sundar, Durai; Kumar, Lalit; Sharma, Atul

doi:10.1186/s13148-017-0356-0

Table 2 Comparison of mRNA levels of selected genes (median ∆Cq and median fold change) as assessed by real time RQ-PCR in CLL (n = 93; unmutated = 39; mutated = 54) and CD19+ sorted B-cells from healthy individuals (n = 10)

From: Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia

Comparison of levels of mRNA expression of selected genes in CLL
S.No.	Gene	CLL Vs. normal				Mutated CLL Vs. unmutated CLL
		Group	Median ∆Cq	Median fold change	p value	IGHV Mutation status	Median ∆Cq	Median fold change	p value
1.	CRY1	CLL	8.61	0.75	0.91	Mutated	9.8	0.31	<0.001
1.	CRY1	19+ Normal	8.29	0.75	0.91	Unmutated	7.46	1.73	<0.001
2.	MEIS1	CLL	13.03	0.07	0.01	Mutated	12.85	0.05	0.85
2.	MEIS1	19+ Normal	8.87	0.07	0.01	Unmutated	12.63	0.06	0.85
3.	ID4	CLL	13.75	4.37	0.03	Mutated	13.51	3.89	0.45
3.	ID4	19+ Normal	15.7	4.37	0.03	Unmutated	13.71	3.2	0.45
4.	TNRC18	CLL	13.21	0.64	0.43	Mutated	12.93	0.62	0.6
4.	TNRC18	19+ Normal	12.53	0.64	0.43	Unmutated	13.34	0.59	0.6
5.	NFATC1	CLL	8.43	0.5	0.47	Mutated	8.86	0.39	0.37
5.	NFATC1	19+ Normal	7.54	0.5	0.47	Unmutated	8.37	0.57	0.37
6.	CDK6	CLL	12.65	0.2	0.02	Mutated	12.65	0.25	0.7
6.	CDK6	19+ Normal	10.48	0.2	0.02	Unmutated	12.65	0.26	0.7
7.	VIPR1	CLL	6.62	7.9	0.04	Mutated	6.5	6.96	0.32
7.	VIPR1	19+ Normal	9.34	7.9	0.04	Unmutated	5.98	11.4	0.32
8.	SPRY1	CLL	12.75	0.04	<0.001	Mutated	12.18	0.05	0.28
8.	SPRY1	19+ Normal	8.49	0.04	<0.001	Unmutated	12.7	0.03	0.28
9.	PAX9	CLL	12.29	0.81	0.66	Mutated	12.8	0.37	<0.001
9.	PAX9	19+ Normal	11.61	0.81	0.66	Unmutated	9.28	4.61	<0.001
10.	PMEPA	CLL	12.33	0.01	<0.001	Mutated	12.32	0.01	0.47
10.	PMEPA	19+ Normal	5.52	0.01	<0.001	Unmutated	11.72	0.01	0.47
11.	TBX2	CLL	16.92	0.1	0.004	Mutated	16.42	0.08	0.67
11.	TBX2	19+ Normal	13.45	0.1	0.004	Unmutated	16.91	0.08	0.67
12.	TSHZ3	CLL	10.9	1.19	0.81	Mutated	10.57	1.15	0.56
12.	TSHZ3	19+ Normal	10.97	1.19	0.81	Unmutated	11.18	0.82	0.56
13.	BIK	CLL	8.27	0.4	0.5	Mutated	8.4	0.44	0.54
13.	BIK	19+ Normal	7.26	0.4	0.5	Unmutated	8.08	0.53	0.54
14.	SPRY2	CLL	10.2	6.2	0.02	Mutated	9.78	6.59	0.42
14.	SPRY2	19+ Normal	12.4	6.2	0.02	Unmutated	10.26	4.6	0.42
15.	AXIN2	CLL	9.8	6.3	0.23	Mutated	9.2	4.79	0.56
15.	AXIN2	19+ Normal	11.77	6.3	0.23	Unmutated	8.91	6.66	0.56
16.	SOX7	CLL	11.93	0.18	0.02	Mutated	11.65	0.18	0.99
16.	SOX7	19+ Normal	9.23	0.18	0.02	Unmutated	11.92	0.16	0.99
17.	RIC8B	CLL	8.77	1.85	0.38	Mutated	8.59	1.85	0.78
17.	RIC8B	19+ Normal	9.61	1.85	0.38	Unmutated	8.72	1.75	0.78

The statistically significant p values are shown in italics

Back to article page

ISSN: 1868-7083

Contact us

Submission enquiries: avalyn.villar@springernature.com
General enquiries: info@biomedcentral.com

Clinical Epigenetics

Contact us